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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6809 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2011-08-25 17:01:01 +00:00
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doc/Developers.pdf → doc/Developer.pdf
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doc/Manual.txt
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@ -40,7 +40,7 @@ The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated
about once per month. This is because it is large, and we don't want
it to be part of very patch. :l
There is also a "Developers.pdf"_Developers.pdf file in the doc
There is also a "Developer.pdf"_Developer.pdf file in the doc
directory, which describes the internal structure and algorithms of
LAMMPS. :ule,l

26
doc/Section_accelerate.html
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@ -58,9 +58,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
</P>
<P>To see what styles are currently available in each of the accelerated
packages, see <A HREF = "Section_commands.html#3_5">this section</A> of the manual.
A list of accelerated styles is included in the pair, fix, compute,
and kspace sections.
packages, see <A HREF = "Section_commands.html#cmd_5">this section</A> of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
</P>
<P>The following sections explain:
</P>
@ -73,17 +73,17 @@ and kspace sections.
<P>The final section compares and contrasts the GPU and USER-CUDA
packages, since they are both designed to use NVIDIA GPU hardware.
</P>
5.1 <A HREF = "#5_1">OPT package</A><BR>
5.2 <A HREF = "#5_2">USER-OMP package</A><BR>
5.3 <A HREF = "#5_3">GPU package</A><BR>
5.4 <A HREF = "#5_4">USER-CUDA package</A><BR>
5.5 <A HREF = "#5_4">Comparison of GPU and USER-CUDA packages</A> <BR>
5.1 <A HREF = "#acc_1">OPT package</A><BR>
5.2 <A HREF = "#acc_2">USER-OMP package</A><BR>
5.3 <A HREF = "#acc_3">GPU package</A><BR>
5.4 <A HREF = "#acc_4">USER-CUDA package</A><BR>
5.5 <A HREF = "#acc_5">Comparison of GPU and USER-CUDA packages</A> <BR>
<HR>
<HR>
<H4><A NAME = "5_1"></A>5.1 OPT package
<H4><A NAME = "acc_1"></A>5.1 OPT package
</H4>
<P>The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@ -112,7 +112,7 @@ to 20% savings.
<HR>
<H4><A NAME = "5_2"></A>5.2 USER-OMP package
<H4><A NAME = "acc_2"></A>5.2 USER-OMP package
</H4>
<P>This section will be written when the USER-OMP package is released
in main LAMMPS.
@ -121,7 +121,7 @@ in main LAMMPS.
<HR>
<H4><A NAME = "5_3"></A>5.3 GPU package
<H4><A NAME = "acc_3"></A>5.3 GPU package
</H4>
<P>The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
@ -263,7 +263,7 @@ requires that your GPU card support double precision.
<HR>
<H4><A NAME = "5_4"></A>5.4 USER-CUDA package
<H4><A NAME = "acc_4"></A>5.4 USER-CUDA package
</H4>
<P>The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
@ -396,7 +396,7 @@ occurs, the faster your simulation will run.
<HR>
<H4><A NAME = "5_5"></A>5.5 Comparison of GPU and USER-CUDA packages
<H4><A NAME = "acc_5"></A>5.5 Comparison of GPU and USER-CUDA packages
</H4>
<P>Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.

26
doc/Section_accelerate.txt
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@ -55,9 +55,9 @@ The speed-up due to GPU usage depends on a variety of factors, as
discussed below.
To see what styles are currently available in each of the accelerated
packages, see "this section"_Section_commands.html#3_5 of the manual.
A list of accelerated styles is included in the pair, fix, compute,
and kspace sections.
packages, see "this section"_Section_commands.html#cmd_5 of the
manual. A list of accelerated styles is included in the pair, fix,
compute, and kspace sections.
The following sections explain:
@ -70,16 +70,16 @@ speed-ups you can expect :ul
The final section compares and contrasts the GPU and USER-CUDA
packages, since they are both designed to use NVIDIA GPU hardware.
5.1 "OPT package"_#5_1
5.2 "USER-OMP package"_#5_2
5.3 "GPU package"_#5_3
5.4 "USER-CUDA package"_#5_4
5.5 "Comparison of GPU and USER-CUDA packages"_#5_4 :all(b)
5.1 "OPT package"_#acc_1
5.2 "USER-OMP package"_#acc_2
5.3 "GPU package"_#acc_3
5.4 "USER-CUDA package"_#acc_4
5.5 "Comparison of GPU and USER-CUDA packages"_#acc_5 :all(b)
:line
:line
5.1 OPT package :h4,link(5_1)
5.1 OPT package :h4,link(acc_1)
The OPT package was developed by James Fischer (High Performance
Technologies), David Richie, and Vincent Natoli (Stone Ridge
@ -107,7 +107,7 @@ to 20% savings.
:line
:line
5.2 USER-OMP package :h4,link(5_2)
5.2 USER-OMP package :h4,link(acc_2)
This section will be written when the USER-OMP package is released
in main LAMMPS.
@ -115,7 +115,7 @@ in main LAMMPS.
:line
:line
5.3 GPU package :h4,link(5_3)
5.3 GPU package :h4,link(acc_3)
The GPU package was developed by Mike Brown at ORNL. It provides GPU
versions of several pair styles and for long-range Coulombics via the
@ -256,7 +256,7 @@ requires that your GPU card support double precision.
:line
:line
5.4 USER-CUDA package :h4,link(5_4)
5.4 USER-CUDA package :h4,link(acc_4)
The USER-CUDA package was developed by Christian Trott at U Technology
Ilmenau in Germany. It provides NVIDIA GPU versions of many pair
@ -388,7 +388,7 @@ occurs, the faster your simulation will run.
:line
:line
5.5 Comparison of GPU and USER-CUDA packages :h4,link(5_5)
5.5 Comparison of GPU and USER-CUDA packages :h4,link(acc_5)
Both the GPU and USER-CUDA packages accelerate a LAMMPS calculation
using NVIDIA hardware, but they do it in different ways.

30
doc/Section_commands.html
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@ -14,15 +14,15 @@
<P>This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
</P>
3.1 <A HREF = "#3_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#3_2">Parsing rules</A><BR>
3.3 <A HREF = "#3_3">Input script structure</A><BR>
3.4 <A HREF = "#3_4">Commands listed by category</A><BR>
3.5 <A HREF = "#3_5">Commands listed alphabetically</A> <BR>
3.1 <A HREF = "#cmd_1">LAMMPS input script</A><BR>
3.2 <A HREF = "#cmd_2">Parsing rules</A><BR>
3.3 <A HREF = "#cmd_3">Input script structure</A><BR>
3.4 <A HREF = "#cmd_4">Commands listed by category</A><BR>
3.5 <A HREF = "#cmd_5">Commands listed alphabetically</A> <BR>
<HR>
<A NAME = "3_1"></A><H4>3.1 LAMMPS input script
<A NAME = "cmd_1"></A><H4>3.1 LAMMPS input script
</H4>
<P>LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
@ -75,7 +75,7 @@ command lists restrictions on how the command can be used.
</P>
<HR>
<A NAME = "3_2"></A><H4>3.2 Parsing rules
<A NAME = "cmd_2"></A><H4>3.2 Parsing rules
</H4>
<P>Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
@ -134,7 +134,7 @@ allowed, but that should be sufficient for most use cases.
</P>
<HR>
<H4><A NAME = "3_3"></A>3.3 Input script structure
<H4><A NAME = "cmd_3"></A>3.3 Input script structure
</H4>
<P>This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
@ -223,11 +223,11 @@ the <A HREF = "minimize.html">minimize</A> command. A parallel tempering
</P>
<HR>
<A NAME = "3_4"></A><H4>3.4 Commands listed by category
<A NAME = "cmd_4"></A><H4>3.4 Commands listed by category
</H4>
<P>This section lists all LAMMPS commands, grouped by category. The
<A HREF = "#3_5">next section</A> lists the same commands alphabetically. Note that
some style options for some commands are part of specific LAMMPS
<A HREF = "#cmd_5">next section</A> lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -300,12 +300,12 @@ in the command's documentation.
</P>
<HR>
<H4><A NAME = "3_5"></A><A NAME = "comm"></A>3.5 Individual commands
<H4><A NAME = "cmd_5"></A><A NAME = "comm"></A>3.5 Individual commands
</H4>
<P>This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The <A HREF = "#3_4">previous
section</A> lists the same commands, grouped by category. Note that
some style options for some commands are part of specific LAMMPS
listing below of styles within certain commands. The <A HREF = "#cmd_4">previous
section</A> lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions

28
doc/Section_commands.txt
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@ -11,15 +11,15 @@
This section describes how a LAMMPS input script is formatted and what
commands are used to define a LAMMPS simulation.
3.1 "LAMMPS input script"_#3_1
3.2 "Parsing rules"_#3_2
3.3 "Input script structure"_#3_3
3.4 "Commands listed by category"_#3_4
3.5 "Commands listed alphabetically"_#3_5 :all(b)
3.1 "LAMMPS input script"_#cmd_1
3.2 "Parsing rules"_#cmd_2
3.3 "Input script structure"_#cmd_3
3.4 "Commands listed by category"_#cmd_4
3.5 "Commands listed alphabetically"_#cmd_5 :all(b)
:line
3.1 LAMMPS input script :link(3_1),h4
3.1 LAMMPS input script :link(cmd_1),h4
LAMMPS executes by reading commands from a input script (text file),
one line at a time. When the input script ends, LAMMPS exits. Each
@ -72,7 +72,7 @@ command lists restrictions on how the command can be used.
:line
3.2 Parsing rules :link(3_2),h4
3.2 Parsing rules :link(cmd_2),h4
Each non-blank line in the input script is treated as a command.
LAMMPS commands are case sensitive. Command names are lower-case, as
@ -131,7 +131,7 @@ allowed, but that should be sufficient for most use cases.
:line
3.3 Input script structure :h4,link(3_3)
3.3 Input script structure :h4,link(cmd_3)
This section describes the structure of a typical LAMMPS input script.
The "examples" directory in the LAMMPS distribution contains many
@ -220,11 +220,11 @@ the "minimize"_minimize.html command. A parallel tempering
:line
3.4 Commands listed by category :link(3_4),h4
3.4 Commands listed by category :link(cmd_4),h4
This section lists all LAMMPS commands, grouped by category. The
"next section"_#3_5 lists the same commands alphabetically. Note that
some style options for some commands are part of specific LAMMPS
"next section"_#cmd_5 lists the same commands alphabetically. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions
@ -297,12 +297,12 @@ Miscellaneous:
:line
3.5 Individual commands :h4,link(3_5),link(comm)
3.5 Individual commands :h4,link(cmd_5),link(comm)
This section lists all LAMMPS commands alphabetically, with a separate
listing below of styles within certain commands. The "previous
section"_#3_4 lists the same commands, grouped by category. Note that
some style options for some commands are part of specific LAMMPS
section"_#cmd_4 lists the same commands, grouped by category. Note
that some style options for some commands are part of specific LAMMPS
packages, which means they cannot be used unless the package was
included when LAMMPS was built. Not all packages are included in a
default LAMMPS build. These dependencies are listed as Restrictions

14
doc/Section_errors.html
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@ -16,13 +16,13 @@ Section</A>
<P>This section describes the various kinds of errors you can encounter
when using LAMMPS.
</P>
12.1 <A HREF = "#12_1">Common problems</A><BR>
12.2 <A HREF = "#12_2">Reporting bugs</A><BR>
12.3 <A HREF = "#12_3">Error & warning messages</A> <BR>
12.1 <A HREF = "#err_1">Common problems</A><BR>
12.2 <A HREF = "#err_2">Reporting bugs</A><BR>
12.3 <A HREF = "#err_3">Error & warning messages</A> <BR>
<HR>
<A NAME = "12_1"></A><H4>12.1 Common problems
<A NAME = "err_1"></A><H4>12.1 Common problems
</H4>
<P>If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
@ -81,7 +81,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
could be a bug (see <A HREF = "#12_2">this section</A>) or one of the following
could be a bug (see <A HREF = "#err_2">this section</A>) or one of the following
cases:
</P>
<P>LAMMPS runs in the available memory a processor allows to be
@ -112,7 +112,7 @@ buffering or boost the sizes of messages that can be buffered.
</P>
<HR>
<A NAME = "12_2"></A><H4>12.2 Reporting bugs
<A NAME = "err_2"></A><H4>12.2 Reporting bugs
</H4>
<P>If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -142,7 +142,7 @@ causing the problem.
</P>
<HR>
<H4><A NAME = "12_3"></A>12.3 Error & warning messages
<H4><A NAME = "err_3"></A>12.3 Error & warning messages
</H4>
<P>These are two alphabetic lists of the <A HREF = "#error">ERROR</A> and
<A HREF = "#warn">WARNING</A> messages LAMMPS prints out and the reason why. If the

14
doc/Section_errors.txt
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@ -13,13 +13,13 @@ Section"_Section_history.html :c
This section describes the various kinds of errors you can encounter
when using LAMMPS.
12.1 "Common problems"_#12_1
12.2 "Reporting bugs"_#12_2
12.3 "Error & warning messages"_#12_3 :all(b)
12.1 "Common problems"_#err_1
12.2 "Reporting bugs"_#err_2
12.3 "Error & warning messages"_#err_3 :all(b)
:line
12.1 Common problems :link(12_1),h4
12.1 Common problems :link(err_1),h4
If two LAMMPS runs do not produce the same answer on different
machines or different numbers of processors, this is typically not a
@ -78,7 +78,7 @@ decide if the WARNING is important or not. A WARNING message that is
generated in the middle of a run is only printed to the screen, not to
the logfile, to avoid cluttering up thermodynamic output. If LAMMPS
crashes or hangs without spitting out an error message first then it
could be a bug (see "this section"_#12_2) or one of the following
could be a bug (see "this section"_#err_2) or one of the following
cases:
LAMMPS runs in the available memory a processor allows to be
@ -109,7 +109,7 @@ buffering or boost the sizes of messages that can be buffered.
:line
12.2 Reporting bugs :link(12_2),h4
12.2 Reporting bugs :link(err_2),h4
If you are confident that you have found a bug in LAMMPS, follow these
steps.
@ -139,7 +139,7 @@ As a last resort, you can send an email directly to the
:line
12.3 Error & warning messages :h4,link(12_3)
12.3 Error & warning messages :h4,link(err_3)
These are two alphabetic lists of the "ERROR"_#error and
"WARNING"_#warn messages LAMMPS prints out and the reason why. If the

12
doc/Section_history.html
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@ -1,5 +1,7 @@
<HTML>
<CENTER><A HREF = "Section_errors.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Manual.html">Next Section</A>
<CENTER><A HREF = "Section_errors.html">Previous Section</A> - <A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> -
<A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A> - <A HREF = "Manual.html">Next
Section</A>
</CENTER>
@ -15,12 +17,12 @@
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
</P>
13.1 <A HREF = "#13_1">Coming attractions</A><BR>
13.2 <A HREF = "#13_2">Past versions</A> <BR>
13.1 <A HREF = "#hist_1">Coming attractions</A><BR>
13.2 <A HREF = "#hist_2">Past versions</A> <BR>
<HR>
<H4><A NAME = "13_1"></A>13.1 Coming attractions
<H4><A NAME = "hist_1"></A>13.1 Coming attractions
</H4>
<P>The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes developed at Sandia. These include
@ -49,7 +51,7 @@ page</A> on the LAMMPS WWW site for more details.
</UL>
<HR>
<H4><A NAME = "13_2"></A>13.2 Past versions
<H4><A NAME = "hist_2"></A>13.2 Past versions
</H4>
<P>LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

12
doc/Section_history.txt
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@ -1,4 +1,6 @@
"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Manual.html :c
"Previous Section"_Section_errors.html - "LAMMPS WWW Site"_lws -
"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
Section"_Manual.html :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
@ -12,12 +14,12 @@ This section lists features we are planning to add to LAMMPS, features
of previous versions of LAMMPS, and features of other parallel
molecular dynamics codes I've distributed.
13.1 "Coming attractions"_#13_1
13.2 "Past versions"_#13_2 :all(b)
13.1 "Coming attractions"_#hist_1
13.2 "Past versions"_#hist_2 :all(b)
:line
13.1 Coming attractions :h4,link(13_1)
13.1 Coming attractions :h4,link(hist_1)
The current version of LAMMPS incorporates nearly all the features
from previous parallel MD codes developed at Sandia. These include
@ -46,7 +48,7 @@ Direct Simulation Monte Carlo - DSMC :ul
:line
13.2 Past versions :h4,link(13_2)
13.2 Past versions :h4,link(hist_2)
LAMMPS development began in the mid 1990s under a cooperative research
& development agreement (CRADA) between two DOE labs (Sandia and LLNL)

100
doc/Section_howto.html
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@ -14,27 +14,27 @@
<P>The following sections describe how to use various options within
LAMMPS.
</P>
6.1 <A HREF = "#6_1">Restarting a simulation</A><BR>
6.2 <A HREF = "#6_2">2d simulations</A><BR>
6.3 <A HREF = "#6_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
6.4 <A HREF = "#6_4">Running multiple simulations from one input script</A><BR>
6.5 <A HREF = "#6_5">Multi-replica simulations</A><BR>
6.6 <A HREF = "#6_6">Granular models</A><BR>
6.7 <A HREF = "#6_7">TIP3P water model</A><BR>
6.8 <A HREF = "#6_8">TIP4P water model</A><BR>
6.9 <A HREF = "#6_9">SPC water model</A><BR>
6.10 <A HREF = "#6_10">Coupling LAMMPS to other codes</A><BR>
6.11 <A HREF = "#6_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#6_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#6_13">NEMD simulations</A><BR>
6.14 <A HREF = "#6_14">Extended spherical and aspherical particles</A><BR>
6.15 <A HREF = "#6_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#6_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#6_17">Walls</A><BR>
6.18 <A HREF = "#6_18">Elastic constants</A><BR>
6.19 <A HREF = "#6_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#6_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#6_21">Calculating viscosity</A> <BR>
6.1 <A HREF = "#howto_1">Restarting a simulation</A><BR>
6.2 <A HREF = "#howto_2">2d simulations</A><BR>
6.3 <A HREF = "#howto_3">CHARMM, AMBER, and DREIDING force fields</A><BR>
6.4 <A HREF = "#howto_4">Running multiple simulations from one input script</A><BR>
6.5 <A HREF = "#howto_5">Multi-replica simulations</A><BR>
6.6 <A HREF = "#howto_6">Granular models</A><BR>
6.7 <A HREF = "#howto_7">TIP3P water model</A><BR>
6.8 <A HREF = "#howto_8">TIP4P water model</A><BR>
6.9 <A HREF = "#howto_9">SPC water model</A><BR>
6.10 <A HREF = "#howto_10">Coupling LAMMPS to other codes</A><BR>
6.11 <A HREF = "#howto_11">Visualizing LAMMPS snapshots</A><BR>
6.12 <A HREF = "#howto_12">Triclinic (non-orthogonal) simulation boxes</A><BR>
6.13 <A HREF = "#howto_13">NEMD simulations</A><BR>
6.14 <A HREF = "#howto_14">Extended spherical and aspherical particles</A><BR>
6.15 <A HREF = "#howto_15">Output from LAMMPS (thermo, dumps, computes, fixes, variables)</A><BR>
6.16 <A HREF = "#howto_16">Thermostatting, barostatting and computing temperature</A><BR>
6.17 <A HREF = "#howto_17">Walls</A><BR>
6.18 <A HREF = "#howto_18">Elastic constants</A><BR>
6.19 <A HREF = "#howto_19">Library interface to LAMMPS</A><BR>
6.20 <A HREF = "#howto_20">Calculating thermal conductivity</A><BR>
6.21 <A HREF = "#howto_21">Calculating viscosity</A> <BR>
<P>The example input scripts included in the LAMMPS distribution and
highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@ -42,7 +42,7 @@ setup and run various kinds of simulations.
</P>
<HR>
<A NAME = "6_1"></A><H4>6.1 Restarting a simulation
<A NAME = "howto_1"></A><H4>6.1 Restarting a simulation
</H4>
<P>There are 3 ways to continue a long LAMMPS simulation. Multiple
<A HREF = "run.html">run</A> commands can be used in the same input script. Each
@ -134,7 +134,7 @@ but not in data files.
</P>
<HR>
<A NAME = "6_2"></A><H4>6.2 2d simulations
<A NAME = "howto_2"></A><H4>6.2 2d simulations
</H4>
<P>Use the <A HREF = "dimension.html">dimension</A> command to specify a 2d simulation.
</P>
@ -169,7 +169,7 @@ the same as in 3d.
</P>
<HR>
<A NAME = "6_3"></A><H4>6.3 CHARMM, AMBER, and DREIDING force fields
<A NAME = "howto_3"></A><H4>6.3 CHARMM, AMBER, and DREIDING force fields
</H4>
<P>A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
@ -246,7 +246,7 @@ documentation for the formula it computes.
</UL>
<HR>
<A NAME = "6_4"></A><H4>6.4 Running multiple simulations from one input script
<A NAME = "howto_4"></A><H4>6.4 Running multiple simulations from one input script
</H4>
<P>This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
@ -334,7 +334,7 @@ the 4th simulation, and so forth, until all 8 were completed.
</P>
<HR>
<A NAME = "6_5"></A><H4>6.5 Multi-replica simulations
<A NAME = "howto_5"></A><H4>6.5 Multi-replica simulations
</H4>
<P>Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
@ -381,7 +381,7 @@ physical processors.
</P>
<HR>
<A NAME = "6_6"></A><H4>6.6 Granular models
<A NAME = "howto_6"></A><H4>6.6 Granular models
</H4>
<P>Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
@ -398,7 +398,7 @@ the following commands:
</P>
<UL><LI><A HREF = "compute_erotate_sphere.html">compute erotate/sphere</A>
</UL>
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#6_15">output with
<P>calculates rotational kinetic energy which can be <A HREF = "Section_howto.html#howto_15">output with
thermodynamic info</A>.
</P>
<P>Use one of these 3 pair potentials, which compute forces and torques
@ -426,7 +426,7 @@ computations between frozen atoms by using this command:
</UL>
<HR>
<A NAME = "6_7"></A><H4>6.7 TIP3P water model
<A NAME = "howto_7"></A><H4>6.7 TIP3P water model
</H4>
<P>The TIP3P water model as implemented in CHARMM
<A HREF = "#MacKerell">(MacKerell)</A> specifies a 3-site rigid water molecule with
@ -486,7 +486,7 @@ models</A>.
</P>
<HR>
<A NAME = "6_8"></A><H4>6.8 TIP4P water model
<A NAME = "howto_8"></A><H4>6.8 TIP4P water model
</H4>
<P>The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
@ -545,7 +545,7 @@ models</A>.
</P>
<HR>
<A NAME = "6_9"></A><H4>6.9 SPC water model
<A NAME = "howto_9"></A><H4>6.9 SPC water model
</H4>
<P>The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@ -590,7 +590,7 @@ models</A>.
</P>
<HR>
<A NAME = "6_10"></A><H4>6.10 Coupling LAMMPS to other codes
<A NAME = "howto_10"></A><H4>6.10 Coupling LAMMPS to other codes
</H4>
<P>LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
@ -673,7 +673,7 @@ the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#6_19">this section</A> of the manual
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the manual
for a description of the interface and how to extend it for your
needs.
</P>
@ -690,7 +690,7 @@ instances of LAMMPS to perform different calculations.
</P>
<HR>
<A NAME = "6_11"></A><H4>6.11 Visualizing LAMMPS snapshots
<A NAME = "howto_11"></A><H4>6.11 Visualizing LAMMPS snapshots
</H4>
<P>LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
@ -749,7 +749,7 @@ See the <A HREF = "dump.html">dump</A> command for more information on XTC files
<HR>
<A NAME = "6_12"></A><H4>6.12 Triclinic (non-orthogonal) simulation boxes
<A NAME = "howto_12"></A><H4>6.12 Triclinic (non-orthogonal) simulation boxes
</H4>
<P>By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The <A HREF = "boundary.html">boundary</A> command sets the boundary
@ -882,7 +882,7 @@ on non-equilibrium MD (NEMD) simulations.
</P>
<HR>
<A NAME = "6_13"></A><H4>6.13 NEMD simulations
<A NAME = "howto_13"></A><H4>6.13 NEMD simulations
</H4>
<P>Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
@ -920,7 +920,7 @@ profile consistent with the applied shear strain rate.
</P>
<HR>
<A NAME = "6_14"></A><H4>6.14 Extended spherical and aspherical particles
<A NAME = "howto_14"></A><H4>6.14 Extended spherical and aspherical particles
</H4>
<P>Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size
@ -1100,7 +1100,7 @@ particles are point masses.
</P>
<HR>
<A NAME = "6_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
<A NAME = "howto_15"></A><H4>6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables)
</H4>
<P>There are four basic kinds of LAMMPS output:
</P>
@ -1394,7 +1394,7 @@ vector input could be a column of an array.
<HR>
<A NAME = "6_16"></A><H4>6.16 Thermostatting, barostatting, and computing temperature
<A NAME = "howto_16"></A><H4>6.16 Thermostatting, barostatting, and computing temperature
</H4>
<P>Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
@ -1455,7 +1455,7 @@ thermostatting can be invoked via the <I>dpd/tstat</I> pair style:
<P><A HREF = "fix_nh.html">Fix nvt</A> only thermostats the translational velocity of
particles. <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the <A HREF = "#6_13">NEMD
integrates the SLLOD equations of motion. See the <A HREF = "#howto_13">NEMD
simulations</A> section of this page for further details. <A HREF = "fix_nvt_sphere.html">Fix
nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
nvt/asphere</A> thermostat not only translation
@ -1545,7 +1545,7 @@ thermodynamic output.
</P>
<HR>
<A NAME = "6_17"></A><H4>6.17 Walls
<A NAME = "howto_17"></A><H4>6.17 Walls
</H4>
<P>Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
@ -1619,7 +1619,7 @@ frictional walls, as well as triangulated surfaces.
</P>
<HR>
<A NAME = "6_18"></A><H4>6.18 Elastic constants
<A NAME = "howto_18"></A><H4>6.18 Elastic constants
</H4>
<P>Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
@ -1655,11 +1655,11 @@ converge and requires careful post-processing <A HREF = "#Shinoda">(Shinoda)</A>
</P>
<HR>
<A NAME = "6_19"></A><H4>6.19 Library interface to LAMMPS
<A NAME = "howto_19"></A><H4>6.19 Library interface to LAMMPS
</H4>
<P>As described in <A HREF = "Section_start.html#start_4">this section</A>, LAMMPS can
be built as a library, so that it can be called by another code, used
in a <A HREF = "Section_howto.html#6_10">coupled manner</A> with other codes, or
in a <A HREF = "Section_howto.html#howto_10">coupled manner</A> with other codes, or
driven through a <A HREF = "Section_python.html">Python interface</A>.
</P>
<P>All of these methodologies use a C-style interface to LAMMPS that is
@ -1736,10 +1736,10 @@ grab data from LAMMPS, change it, and put it back into LAMMPS.
</P>
<HR>
<A NAME = "6_20"></A><H4>6.20 Calculating thermal conductivity
<A NAME = "howto_20"></A><H4>6.20 Calculating thermal conductivity
</H4>
<P>The thermal conductivity kappa of a material can be measured in at
least 3 ways using various options in LAMMPS. (See <A HREF = "Section_howto.html#6_21">this
least 3 ways using various options in LAMMPS. (See <A HREF = "Section_howto.html#howto_21">this
section</A> of the manual for an analogous
discussion for viscosity). The thermal conducitivity tensor kappa is
a measure of the propensity of a material to transmit heat energy in a
@ -1756,7 +1756,7 @@ scalar.
<P>The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a <A HREF = "Section_howto.html#6_13">thermostatting fix</A>, the energy added
with a <A HREF = "Section_howto.html#howto_13">thermostatting fix</A>, the energy added
to the hot region should equal the energy subtracted from the cold
region and be proportional to the heat flux moving between the
regions. See the paper by <A HREF = "#Ikeshoji">Ikeshoji and Hafskjold</A> for
@ -1801,10 +1801,10 @@ formalism.
</P>
<HR>
<A NAME = "6_21"></A><H4>6.21 Calculating viscosity
<A NAME = "howto_21"></A><H4>6.21 Calculating viscosity
</H4>
<P>The shear viscosity eta of a fluid can be measured in at least 3 ways
using various options in LAMMPS. (See <A HREF = "Section_howto.html#6_20">this
using various options in LAMMPS. (See <A HREF = "Section_howto.html#howto_20">this
section</A> of the manual for an analogous
discussion for thermal conductivity). Eta is a measure of the
propensity of a fluid to transmit momentum in a direction
@ -1830,7 +1830,7 @@ y-direction of the Vx component of fluid motion or grad(Vstream) =
dVx/dy. In this case, the Pxy off-diagonal component of the pressure
or stress tensor, as calculated by the <A HREF = "compute_pressure.html">compute
pressure</A> command, can also be monitored, which
is the J term in the equation above. See <A HREF = "Section_howto.html#6_13">this
is the J term in the equation above. See <A HREF = "Section_howto.html#howto_13">this
section</A> of the manual for details on NEMD
simulations.
</P>

100
doc/Section_howto.txt
View File

@ -11,27 +11,27 @@
The following sections describe how to use various options within
LAMMPS.
6.1 "Restarting a simulation"_#6_1
6.2 "2d simulations"_#6_2
6.3 "CHARMM, AMBER, and DREIDING force fields"_#6_3
6.4 "Running multiple simulations from one input script"_#6_4
6.5 "Multi-replica simulations"_#6_5
6.6 "Granular models"_#6_6
6.7 "TIP3P water model"_#6_7
6.8 "TIP4P water model"_#6_8
6.9 "SPC water model"_#6_9
6.10 "Coupling LAMMPS to other codes"_#6_10
6.11 "Visualizing LAMMPS snapshots"_#6_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#6_12
6.13 "NEMD simulations"_#6_13
6.14 "Extended spherical and aspherical particles"_#6_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#6_15
6.16 "Thermostatting, barostatting and computing temperature"_#6_16
6.17 "Walls"_#6_17
6.18 "Elastic constants"_#6_18
6.19 "Library interface to LAMMPS"_#6_19
6.20 "Calculating thermal conductivity"_#6_20
6.21 "Calculating viscosity"_#6_21 :all(b)
6.1 "Restarting a simulation"_#howto_1
6.2 "2d simulations"_#howto_2
6.3 "CHARMM, AMBER, and DREIDING force fields"_#howto_3
6.4 "Running multiple simulations from one input script"_#howto_4
6.5 "Multi-replica simulations"_#howto_5
6.6 "Granular models"_#howto_6
6.7 "TIP3P water model"_#howto_7
6.8 "TIP4P water model"_#howto_8
6.9 "SPC water model"_#howto_9
6.10 "Coupling LAMMPS to other codes"_#howto_10
6.11 "Visualizing LAMMPS snapshots"_#howto_11
6.12 "Triclinic (non-orthogonal) simulation boxes"_#howto_12
6.13 "NEMD simulations"_#howto_13
6.14 "Extended spherical and aspherical particles"_#howto_14
6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_#howto_15
6.16 "Thermostatting, barostatting and computing temperature"_#howto_16
6.17 "Walls"_#howto_17
6.18 "Elastic constants"_#howto_18
6.19 "Library interface to LAMMPS"_#howto_19
6.20 "Calculating thermal conductivity"_#howto_20
6.21 "Calculating viscosity"_#howto_21 :all(b)
The example input scripts included in the LAMMPS distribution and
highlighted in "this section"_Section_example.html also show how to
@ -39,7 +39,7 @@ setup and run various kinds of simulations.
:line
6.1 Restarting a simulation :link(6_1),h4
6.1 Restarting a simulation :link(howto_1),h4
There are 3 ways to continue a long LAMMPS simulation. Multiple
"run"_run.html commands can be used in the same input script. Each
@ -131,7 +131,7 @@ but not in data files.
:line
6.2 2d simulations :link(6_2),h4
6.2 2d simulations :link(howto_2),h4
Use the "dimension"_dimension.html command to specify a 2d simulation.
@ -166,7 +166,7 @@ the same as in 3d.
:line
6.3 CHARMM, AMBER, and DREIDING force fields :link(6_3),h4
6.3 CHARMM, AMBER, and DREIDING force fields :link(howto_3),h4
A force field has 2 parts: the formulas that define it and the
coefficients used for a particular system. Here we only discuss
@ -242,7 +242,7 @@ documentation for the formula it computes.
:line
6.4 Running multiple simulations from one input script :link(6_4),h4
6.4 Running multiple simulations from one input script :link(howto_4),h4
This can be done in several ways. See the documentation for
individual commands for more details on how these examples work.
@ -330,7 +330,7 @@ the 4th simulation, and so forth, until all 8 were completed.
:line
6.5 Multi-replica simulations :link(6_5),h4
6.5 Multi-replica simulations :link(howto_5),h4
Several commands in LAMMPS run mutli-replica simulations, meaning
that multiple instances (replicas) of your simulation are run
@ -377,7 +377,7 @@ physical processors.
:line
6.6 Granular models :link(6_6),h4
6.6 Granular models :link(howto_6),h4
Granular system are composed of spherical particles with a diameter,
as opposed to point particles. This means they have an angular
@ -395,7 +395,7 @@ This compute
"compute erotate/sphere"_compute_erotate_sphere.html :ul
calculates rotational kinetic energy which can be "output with
thermodynamic info"_Section_howto.html#6_15.
thermodynamic info"_Section_howto.html#howto_15.
Use one of these 3 pair potentials, which compute forces and torques
between interacting pairs of particles:
@ -422,7 +422,7 @@ computations between frozen atoms by using this command:
:line
6.7 TIP3P water model :link(6_7),h4
6.7 TIP3P water model :link(howto_7),h4
The TIP3P water model as implemented in CHARMM
"(MacKerell)"_#MacKerell specifies a 3-site rigid water molecule with
@ -482,7 +482,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.8 TIP4P water model :link(6_8),h4
6.8 TIP4P water model :link(howto_8),h4
The four-point TIP4P rigid water model extends the traditional
three-point TIP3P model by adding an additional site, usually
@ -541,7 +541,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.9 SPC water model :link(6_9),h4
6.9 SPC water model :link(howto_9),h4
The SPC water model specifies a 3-site rigid water molecule with
charges and Lennard-Jones parameters assigned to each of the 3 atoms.
@ -586,7 +586,7 @@ models"_http://en.wikipedia.org/wiki/Water_model.
:line
6.10 Coupling LAMMPS to other codes :link(6_10),h4
6.10 Coupling LAMMPS to other codes :link(howto_10),h4
LAMMPS is designed to allow it to be coupled to other codes. For
example, a quantum mechanics code might compute forces on a subset of
@ -668,7 +668,7 @@ the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#6_19 of the manual
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the manual
for a description of the interface and how to extend it for your
needs.
@ -685,7 +685,7 @@ instances of LAMMPS to perform different calculations.
:line
6.11 Visualizing LAMMPS snapshots :link(6_11),h4
6.11 Visualizing LAMMPS snapshots :link(howto_11),h4
LAMMPS itself does not do visualization, but snapshots from LAMMPS
simulations can be visualized (and analyzed) in a variety of ways.
@ -741,7 +741,7 @@ See the "dump"_dump.html command for more information on XTC files.
:line
6.12 Triclinic (non-orthogonal) simulation boxes :link(6_12),h4
6.12 Triclinic (non-orthogonal) simulation boxes :link(howto_12),h4
By default, LAMMPS uses an orthogonal simulation box to encompass the
particles. The "boundary"_boundary.html command sets the boundary
@ -874,7 +874,7 @@ on non-equilibrium MD (NEMD) simulations.
:line
6.13 NEMD simulations :link(6_13),h4
6.13 NEMD simulations :link(howto_13),h4
Non-equilibrium molecular dynamics or NEMD simulations are typically
used to measure a fluid's rheological properties such as viscosity.
@ -912,7 +912,7 @@ An alternative method for calculating viscosities is provided via the
:line
6.14 Extended spherical and aspherical particles :link(6_14),h4
6.14 Extended spherical and aspherical particles :link(howto_14),h4
Typical MD models treat atoms or particles as point masses.
Sometimes, however, it is desirable to have a model with finite-size
@ -1092,7 +1092,7 @@ particles are point masses.
:line
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(6_15),h4
6.15 Output from LAMMPS (thermo, dumps, computes, fixes, variables) :link(howto_15),h4
There are four basic kinds of LAMMPS output:
@ -1382,7 +1382,7 @@ Command: Input: Output:
:line
6.16 Thermostatting, barostatting, and computing temperature :link(6_16),h4
6.16 Thermostatting, barostatting, and computing temperature :link(howto_16),h4
Thermostatting means controlling the temperature of particles in an MD
simulation. Barostatting means controlling the pressure. Since the
@ -1444,7 +1444,7 @@ thermostatting can be invoked via the {dpd/tstat} pair style:
particles. "Fix nvt/sllod"_fix_nvt_sllod.html also does this, except
that it subtracts out a velocity bias due to a deforming box and
integrates the SLLOD equations of motion. See the "NEMD
simulations"_#6_13 section of this page for further details. "Fix
simulations"_#howto_13 section of this page for further details. "Fix
nvt/sphere"_fix_nvt_sphere.html and "fix
nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
velocities but also rotational velocities for spherical and aspherical
@ -1533,7 +1533,7 @@ thermodynamic output.
:line
6.17 Walls :link(6_17),h4
6.17 Walls :link(howto_17),h4
Walls in an MD simulation are typically used to bound particle motion,
i.e. to serve as a boundary condition.
@ -1607,7 +1607,7 @@ frictional walls, as well as triangulated surfaces.
:line
6.18 Elastic constants :link(6_18),h4
6.18 Elastic constants :link(howto_18),h4
Elastic constants characterize the stiffness of a material. The formal
definition is provided by the linear relation that holds between the
@ -1643,11 +1643,11 @@ converge and requires careful post-processing "(Shinoda)"_#Shinoda
:line
6.19 Library interface to LAMMPS :link(6_19),h4
6.19 Library interface to LAMMPS :link(howto_19),h4
As described in "this section"_Section_start.html#start_4, LAMMPS can
be built as a library, so that it can be called by another code, used
in a "coupled manner"_Section_howto.html#6_10 with other codes, or
in a "coupled manner"_Section_howto.html#howto_10 with other codes, or
driven through a "Python interface"_Section_python.html.
All of these methodologies use a C-style interface to LAMMPS that is
@ -1724,11 +1724,11 @@ grab data from LAMMPS, change it, and put it back into LAMMPS.
:line
6.20 Calculating thermal conductivity :link(6_20),h4
6.20 Calculating thermal conductivity :link(howto_20),h4
The thermal conductivity kappa of a material can be measured in at
least 3 ways using various options in LAMMPS. (See "this
section"_Section_howto.html#6_21 of the manual for an analogous
section"_Section_howto.html#howto_21 of the manual for an analogous
discussion for viscosity). The thermal conducitivity tensor kappa is
a measure of the propensity of a material to transmit heat energy in a
diffusive manner as given by Fourier's law
@ -1744,7 +1744,7 @@ scalar.
The first method is to setup two thermostatted regions at opposite
ends of a simulation box, or one in the middle and one at the end of a
periodic box. By holding the two regions at different temperatures
with a "thermostatting fix"_Section_howto.html#6_13, the energy added
with a "thermostatting fix"_Section_howto.html#howto_13, the energy added
to the hot region should equal the energy subtracted from the cold
region and be proportional to the heat flux moving between the
regions. See the paper by "Ikeshoji and Hafskjold"_#Ikeshoji for
@ -1789,11 +1789,11 @@ formalism.
:line
6.21 Calculating viscosity :link(6_21),h4
6.21 Calculating viscosity :link(howto_21),h4
The shear viscosity eta of a fluid can be measured in at least 3 ways
using various options in LAMMPS. (See "this
section"_Section_howto.html#6_20 of the manual for an analogous
section"_Section_howto.html#howto_20 of the manual for an analogous
discussion for thermal conductivity). Eta is a measure of the
propensity of a fluid to transmit momentum in a direction
perpendicular to the direction of velocity or momentum flow.
@ -1819,7 +1819,7 @@ dVx/dy. In this case, the Pxy off-diagonal component of the pressure
or stress tensor, as calculated by the "compute
pressure"_compute_pressure.html command, can also be monitored, which
is the J term in the equation above. See "this
section"_Section_howto.html#6_13 of the manual for details on NEMD
section"_Section_howto.html#howto_13 of the manual for details on NEMD
simulations.
The second method is to perform a reverse non-equilibrium MD

2
doc/Section_intro.html
View File

@ -417,7 +417,7 @@ Site</A>, or have a suggestion for something to clarify or include,
send an email to the
<A HREF = "http://lammps.sandia.gov/authors.html">developers</A>.
<LI>If you find a bug, <A HREF = "Section_errors.html#10_2">this section</A> describes
<LI>If you find a bug, <A HREF = "Section_errors.html#err_2">this section</A> describes
how to report it.
<LI>If you publish a paper using LAMMPS results, send the citation (and

2
doc/Section_intro.txt
View File

@ -407,7 +407,7 @@ Site"_lws, or have a suggestion for something to clarify or include,
send an email to the
"developers"_http://lammps.sandia.gov/authors.html. :l
If you find a bug, "this section"_Section_errors.html#10_2 describes
If you find a bug, "this section"_Section_errors.html#err_2 describes
how to report it. :l
If you publish a paper using LAMMPS results, send the citation (and

56
doc/Section_modify.html
View File

@ -121,26 +121,26 @@ details on this at the bottom of this page.
<P>Here are the subsequent topics discussed below, most of which are new
features that can be added in the manner just described:
</P>
10.1 <A HREF = "#10_1">Atom styles</A><BR>
10.2 <A HREF = "#10_2">Bond, angle, dihedral, improper potentials</A><BR>
10.3 <A HREF = "#10_3">Compute styles</A><BR>
10.4 <A HREF = "#10_4">Dump styles</A><BR>
10.5 <A HREF = "#10_5">Dump custom output options</A><BR>
10.6 <A HREF = "#10_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
10.7 <A HREF = "10_7">Input script commands</A><BR>
10.8 <A HREF = "#10_8">Kspace computations</A><BR>
10.9 <A HREF = "#10_9">Minimization styles</A><BR>
10.10 <A HREF = "#10_10">Pairwise potentials</A><BR>
10.11 <A HREF = "#10_11">Region styles</A><BR>
10.12 <A HREF = "#10_12">Thermodynamic output options</A><BR>
10.13 <A HREF = "#10_13">Variable options</A><BR>
10.14 <A HREF = "#10_14">Submitting new features for inclusion in LAMMPS</A> <BR>
10.1 <A HREF = "#mod_1">Atom styles</A><BR>
10.2 <A HREF = "#mod_2">Bond, angle, dihedral, improper potentials</A><BR>
10.3 <A HREF = "#mod_3">Compute styles</A><BR>
10.4 <A HREF = "#mod_4">Dump styles</A><BR>
10.5 <A HREF = "#mod_5">Dump custom output options</A><BR>
10.6 <A HREF = "#mod_6">Fix styles</A> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc<BR>
10.7 <A HREF = "mod_7">Input script commands</A><BR>
10.8 <A HREF = "#mod_8">Kspace computations</A><BR>
10.9 <A HREF = "#mod_9">Minimization styles</A><BR>
10.10 <A HREF = "#mod_10">Pairwise potentials</A><BR>
10.11 <A HREF = "#mod_11">Region styles</A><BR>
10.12 <A HREF = "#mod_12">Thermodynamic output options</A><BR>
10.13 <A HREF = "#mod_13">Variable options</A><BR>
10.14 <A HREF = "#mod_14">Submitting new features for inclusion in LAMMPS</A> <BR>
<HR>
<HR>
<A NAME = "10_1"></A><H4>10.1 Atom styles
<A NAME = "mod_1"></A><H4>10.1 Atom styles
</H4>
<P>Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
@ -190,7 +190,7 @@ modify.
</P>
<HR>
<A NAME = "10_2"></A><H4>10.2 Bond, angle, dihedral, improper potentials
<A NAME = "mod_2"></A><H4>10.2 Bond, angle, dihedral, improper potentials
</H4>
<P>Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
@ -214,7 +214,7 @@ details.
<HR>
<A NAME = "10_3"></A><H4>10.3 Compute styles
<A NAME = "mod_3"></A><H4>10.3 Compute styles
</H4>
<P>Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
@ -242,9 +242,9 @@ class. See compute.h for details.
<HR>
<A NAME = "10_4"></A><H4>10.4 Dump styles
<A NAME = "mod_4"></A><H4>10.4 Dump styles
</H4>
<A NAME = "10_5"></A><H4>10.5 Dump custom output options
<A NAME = "mod_5"></A><H4>10.5 Dump custom output options
</H4>
<P>Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
@ -275,7 +275,7 @@ half-dozen or so locations where code will need to be added.
</P>
<HR>
<A NAME = "10_6"></A><H4>10.6 Fix styles
<A NAME = "mod_6"></A><H4>10.6 Fix styles
</H4>
<P>In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
@ -353,7 +353,7 @@ quantities and/or to be summed to the potential energy of the system.
</P>
<HR>
<A NAME = "10_7"></A><H4>10.7 Input script commands
<A NAME = "mod_7"></A><H4>10.7 Input script commands
</H4>
<P>New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
@ -375,7 +375,7 @@ needed.
</P>
<HR>
<A NAME = "10_8"></A><H4>10.8 Kspace computations
<A NAME = "mod_8"></A><H4>10.8 Kspace computations
</H4>
<P>Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
@ -395,7 +395,7 @@ class. See kspace.h for details.
<HR>
<A NAME = "10_9"></A><H4>10.9 Minimization styles
<A NAME = "mod_9"></A><H4>10.9 Minimization styles
</H4>
<P>Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
@ -414,7 +414,7 @@ class. See min.h for details.
<HR>
<A NAME = "10_10"></A><H4>10.10 Pairwise potentials
<A NAME = "mod_10"></A><H4>10.10 Pairwise potentials
</H4>
<P>Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
@ -443,7 +443,7 @@ includes some optional methods to enable its use with rRESPA.
</P>
<HR>
<A NAME = "10_11"></A><H4>10.11 Region styles
<A NAME = "mod_11"></A><H4>10.11 Region styles
</H4>
<P>Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
@ -461,7 +461,7 @@ class. See region.h for details.
<HR>
<A NAME = "10_12"></A><H4>10.12 Thermodynamic output options
<A NAME = "mod_12"></A><H4>10.12 Thermodynamic output options
</H4>
<P>There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
@ -490,7 +490,7 @@ by adding a new keyword to the thermo command.
</P>
<HR>
<A NAME = "10_13"></A><H4>10.13 Variable options
<A NAME = "mod_13"></A><H4>10.13 Variable options
</H4>
<P>There is one class that computes and stores <A HREF = "variable.html">variable</A>
information in LAMMPS; see the file variable.cpp. The value
@ -532,7 +532,7 @@ then be accessed by variables) was discussed
<HR>
<A NAME = "10_14"></A><H4>10.14 Submitting new features for inclusion in LAMMPS
<A NAME = "mod_14"></A><H4>10.14 Submitting new features for inclusion in LAMMPS
</H4>
<P>We encourage users to submit new features that they add to LAMMPS to
<A HREF = "http://lammps.sandia.gov/authors.html">the developers</A>, especially if

56
doc/Section_modify.txt
View File

@ -118,27 +118,27 @@ details on this at the bottom of this page. :l,ule
Here are the subsequent topics discussed below, most of which are new
features that can be added in the manner just described:
10.1 "Atom styles"_#10_1
10.2 "Bond, angle, dihedral, improper potentials"_#10_2
10.3 "Compute styles"_#10_3
10.4 "Dump styles"_#10_4
10.5 "Dump custom output options"_#10_5
10.6 "Fix styles"_#10_6 which include integrators, \
10.1 "Atom styles"_#mod_1
10.2 "Bond, angle, dihedral, improper potentials"_#mod_2
10.3 "Compute styles"_#mod_3
10.4 "Dump styles"_#mod_4
10.5 "Dump custom output options"_#mod_5
10.6 "Fix styles"_#mod_6 which include integrators, \
temperature and pressure control, force constraints, \
boundary conditions, diagnostic output, etc
10.7 "Input script commands"_10_7
10.8 "Kspace computations"_#10_8
10.9 "Minimization styles"_#10_9
10.10 "Pairwise potentials"_#10_10
10.11 "Region styles"_#10_11
10.12 "Thermodynamic output options"_#10_12
10.13 "Variable options"_#10_13
10.14 "Submitting new features for inclusion in LAMMPS"_#10_14 :all(b)
10.7 "Input script commands"_mod_7
10.8 "Kspace computations"_#mod_8
10.9 "Minimization styles"_#mod_9
10.10 "Pairwise potentials"_#mod_10
10.11 "Region styles"_#mod_11
10.12 "Thermodynamic output options"_#mod_12
10.13 "Variable options"_#mod_13
10.14 "Submitting new features for inclusion in LAMMPS"_#mod_14 :all(b)
:line
:line
10.1 Atom styles :link(10_1),h4
10.1 Atom styles :link(mod_1),h4
Classes that define an atom style are derived from the Atom class.
The atom style determines what quantities are associated with an atom.
@ -186,7 +186,7 @@ modify.
:line
10.2 Bond, angle, dihedral, improper potentials :link(10_2),h4
10.2 Bond, angle, dihedral, improper potentials :link(mod_2),h4
Classes that compute molecular interactions are derived from the Bond,
Angle, Dihedral, and Improper classes. New styles can be created to
@ -208,7 +208,7 @@ single: force and energy of a single bond :tb(s=:)
:line
10.3 Compute styles :link(10_3),h4
10.3 Compute styles :link(mod_3),h4
Classes that compute scalar and vector quantities like temperature
and the pressure tensor, as well as classes that compute per-atom
@ -234,8 +234,8 @@ memory_usage: tally memory usage :tb(s=:)
:line
10.4 Dump styles :link(10_4),h4
10.5 Dump custom output options :link(10_5),h4
10.4 Dump styles :link(mod_4),h4
10.5 Dump custom output options :link(mod_5),h4
Classes that dump per-atom info to files are derived from the Dump
class. To dump new quantities or in a new format, a new derived dump
@ -264,7 +264,7 @@ half-dozen or so locations where code will need to be added.
:line
10.6 Fix styles :link(10_6),h4
10.6 Fix styles :link(mod_6),h4
In LAMMPS, a "fix" is any operation that is computed during
timestepping that alters some property of the system. Essentially
@ -340,7 +340,7 @@ quantities and/or to be summed to the potential energy of the system.
:line
10.7 Input script commands :link(10_7),h4
10.7 Input script commands :link(mod_7),h4
New commands can be added to LAMMPS input scripts by adding new
classes that have a "command" method. For example, the create_atoms,
@ -360,7 +360,7 @@ needed.
:line
10.8 Kspace computations :link(10_8),h4
10.8 Kspace computations :link(mod_8),h4
Classes that compute long-range Coulombic interactions via K-space
representations (Ewald, PPPM) are derived from the KSpace class. New
@ -378,7 +378,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
10.9 Minimization styles :link(10_9),h4
10.9 Minimization styles :link(mod_9),h4
Classes that perform energy minimization derived from the Min class.
New styles can be created to add new minimization algorithms to
@ -395,7 +395,7 @@ memory_usage: tally of memory usage :tb(s=:)
:line
10.10 Pairwise potentials :link(10_10),h4
10.10 Pairwise potentials :link(mod_10),h4
Classes that compute pairwise interactions are derived from the Pair
class. In LAMMPS, pairwise calculation include manybody potentials
@ -422,7 +422,7 @@ The inner/middle/outer routines are optional.
:line
10.11 Region styles :link(10_11),h4
10.11 Region styles :link(mod_11),h4
Classes that define geometric regions are derived from the Region
class. Regions are used elsewhere in LAMMPS to group atoms, delete
@ -438,7 +438,7 @@ match: determine whether a point is in the region :tb(s=:)
:line
10.12 Thermodynamic output options :link(10_12),h4
10.12 Thermodynamic output options :link(mod_12),h4
There is one class that computes and prints thermodynamic information
to the screen and log file; see the file thermo.cpp.
@ -467,7 +467,7 @@ by adding a new keyword to the thermo command.
:line
10.13 Variable options :link(10_13),h4
10.13 Variable options :link(mod_13),h4
There is one class that computes and stores "variable"_variable.html
information in LAMMPS; see the file variable.cpp. The value
@ -508,7 +508,7 @@ then be accessed by variables) was discussed
:line
:line
10.14 Submitting new features for inclusion in LAMMPS :link(10_14),h4
10.14 Submitting new features for inclusion in LAMMPS :link(mod_14),h4
We encourage users to submit new features that they add to LAMMPS to
"the developers"_http://lammps.sandia.gov/authors.html, especially if

34
doc/Section_python.html
View File

@ -20,11 +20,11 @@ either from a Python script or interactively from a Python prompt.
<P><A HREF = "http://www.python.org">Python</A> is a powerful scripting and programming
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#4_10">this
together, e.g. to run a coupled or multiscale model. See <A HREF = "Section_howto.html#howto_10">this
section</A> of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See <A HREF = "Section_start.html#start_4">this section</A> about how
to build LAMMPS as a library, and <A HREF = "Section_howto.html#4_19">this
to build LAMMPS as a library, and <A HREF = "Section_howto.html#howto_19">this
section</A> for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
@ -89,13 +89,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
</P>
<UL><LI>11.1 <A HREF = "#11_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#11_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#11_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#11_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#11_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#11_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#11_7">Example Python scripts that use LAMMPS</A>
<UL><LI>11.1 <A HREF = "#py_1">Extending Python with a serial version of LAMMPS</A>
<LI>11.2 <A HREF = "#py_2">Creating a shared MPI library</A>
<LI>11.3 <A HREF = "#py_3">Extending Python with a parallel version of LAMMPS</A>
<LI>11.4 <A HREF = "#py_4">Extending Python with MPI</A>
<LI>11.5 <A HREF = "#py_5">Testing the Python-LAMMPS interface</A>
<LI>11.6 <A HREF = "#py_6">Using LAMMPS from Python</A>
<LI>11.7 <A HREF = "#py_7">Example Python scripts that use LAMMPS</A>
</UL>
<P>Before proceeding, there are 2 items to note.
</P>
@ -135,7 +135,7 @@ LAMMPS wrapper.
<HR>
<A NAME = "11_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
<A NAME = "py_1"></A><H4>11.1 Extending Python with a serial version of LAMMPS
</H4>
<P>From the python directory in the LAMMPS distribution, type
</P>
@ -165,7 +165,7 @@ this, where you should replace "foo" with your directory of choice.
</P>
<HR>
<A NAME = "11_2"></A><H4>11.2 Creating a shared MPI library
<A NAME = "py_2"></A><H4>11.2 Creating a shared MPI library
</H4>
<P>A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -196,7 +196,7 @@ stand-alone code.
</P>
<HR>
<A NAME = "11_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
<A NAME = "py_3"></A><H4>11.3 Extending Python with a parallel version of LAMMPS
</H4>
<P>From the python directory, type
</P>
@ -234,7 +234,7 @@ will be put in the appropriate directory.
</P>
<HR>
<A NAME = "11_4"></A><H4>11.4 Extending Python with MPI
<A NAME = "py_4"></A><H4>11.4 Extending Python with MPI
</H4>
<P>There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -309,7 +309,7 @@ print "Proc %d out of %d procs" % (pypar.rank(),pypar.size())
</P>
<HR>
<A NAME = "11_5"></A><H4>11.5 Testing the Python-LAMMPS interface
<A NAME = "py_5"></A><H4>11.5 Testing the Python-LAMMPS interface
</H4>
<P>Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -403,7 +403,7 @@ Python on a single processor, not in parallel.
<HR>
<A NAME = "11_6"></A><H4>11.6 Using LAMMPS from Python
<A NAME = "py_6"></A><H4>11.6 Using LAMMPS from Python
</H4>
<P>The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -499,7 +499,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See <A HREF = "Section_howto.html#4_15">this section</A> of the manual for a
See <A HREF = "Section_howto.html#howto_15">this section</A> of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
<A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> for a description of what
@ -595,7 +595,7 @@ Python script. Isn't ctypes amazing?
<HR>
<A NAME = "11_7"></A><H4>11.7 Example Python scripts that use LAMMPS
<A NAME = "py_7"></A><H4>11.7 Example Python scripts that use LAMMPS
</H4>
<P>These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of

34
doc/Section_python.txt
View File

@ -18,11 +18,11 @@ either from a Python script or interactively from a Python prompt.
language which can be used to wrap software like LAMMPS and other
packages. It can be used to glue multiple pieces of software
together, e.g. to run a coupled or multiscale model. See "this
section"_Section_howto.html#4_10 of the manual and the couple
section"_Section_howto.html#howto_10 of the manual and the couple
directory of the distribution for more ideas about coupling LAMMPS to
other codes. See "this section"_Section_start.html#start_4 about how
to build LAMMPS as a library, and "this
section"_Section_howto.html#4_19 for a description of the library
section"_Section_howto.html#howto_19 for a description of the library
interface provided in src/library.cpp and src/library.h and how to
extend it for your needs. As described below, that interface is what
is exposed to Python. It is designed to be easy to add functions to.
@ -86,13 +86,13 @@ setup discussion. The next to last sub-section describes the Python
syntax used to invoke LAMMPS. The last sub-section describes example
Python scripts included in the python directory.
11.1 "Extending Python with a serial version of LAMMPS"_#11_1
11.2 "Creating a shared MPI library"_#11_2
11.3 "Extending Python with a parallel version of LAMMPS"_#11_3
11.4 "Extending Python with MPI"_#11_4
11.5 "Testing the Python-LAMMPS interface"_#11_5
11.6 "Using LAMMPS from Python"_#11_6
11.7 "Example Python scripts that use LAMMPS"_#11_7 :ul
11.1 "Extending Python with a serial version of LAMMPS"_#py_1
11.2 "Creating a shared MPI library"_#py_2
11.3 "Extending Python with a parallel version of LAMMPS"_#py_3
11.4 "Extending Python with MPI"_#py_4
11.5 "Testing the Python-LAMMPS interface"_#py_5
11.6 "Using LAMMPS from Python"_#py_6
11.7 "Example Python scripts that use LAMMPS"_#py_7 :ul
Before proceeding, there are 2 items to note.
@ -131,7 +131,7 @@ LAMMPS wrapper.
:line
:line
11.1 Extending Python with a serial version of LAMMPS :link(11_1),h4
11.1 Extending Python with a serial version of LAMMPS :link(py_1),h4
From the python directory in the LAMMPS distribution, type
@ -161,7 +161,7 @@ If these commands are successful, a {lammps.py} and
:line
11.2 Creating a shared MPI library :link(11_2),h4
11.2 Creating a shared MPI library :link(py_2),h4
A shared library is one that is dynamically loadable, which is what
Python requires. On Linux this is a library file that ends in ".so",
@ -192,7 +192,7 @@ stand-alone code.
:line
11.3 Extending Python with a parallel version of LAMMPS :link(11_3),h4
11.3 Extending Python with a parallel version of LAMMPS :link(py_3),h4
From the python directory, type
@ -230,7 +230,7 @@ will be put in the appropriate directory.
:line
11.4 Extending Python with MPI :link(11_4),h4
11.4 Extending Python with MPI :link(py_4),h4
There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.
@ -305,7 +305,7 @@ and see one line of output for each processor you ran on.
:line
11.5 Testing the Python-LAMMPS interface :link(11_5),h4
11.5 Testing the Python-LAMMPS interface :link(py_5),h4
Before using LAMMPS in a Python program, one more step is needed. The
interface to LAMMPS is via the Python ctypes package, which loads the
@ -398,7 +398,7 @@ Python on a single processor, not in parallel.
:line
:line
11.6 Using LAMMPS from Python :link(11_6),h4
11.6 Using LAMMPS from Python :link(py_6),h4
The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a
@ -494,7 +494,7 @@ subscripting. The one exception is that for a fix that calculates a
global vector or array, a single double value from the vector or array
is returned, indexed by I (vector) or I and J (array). I,J are
zero-based indices. The I,J arguments can be left out if not needed.
See "this section"_Section_howto.html#4_15 of the manual for a
See "this section"_Section_howto.html#howto_15 of the manual for a
discussion of global, per-atom, and local data, and of scalar, vector,
and array data types. See the doc pages for individual
"computes"_compute.html and "fixes"_fix.html for a description of what
@ -589,7 +589,7 @@ Python script. Isn't ctypes amazing? :l,ule
:line
:line
11.7 Example Python scripts that use LAMMPS :link(11_7),h4
11.7 Example Python scripts that use LAMMPS :link(py_7),h4
These are the Python scripts included as demos in the python/examples
directory of the LAMMPS distribution, to illustrate the kinds of

26
doc/Section_start.html
View File

@ -682,9 +682,9 @@ build will likely fail.
<H4><A NAME = "start_4"></A>2.4 Building LAMMPS as a library
</H4>
<P>LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See <A HREF = "Section_howto.html#4_10">this
section</A> for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
another application or a scripting language. See <A HREF = "Section_howto.html#howto_10">this
section</A> for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
</P>
<PRE>make makelib
make -f Makefile.lib foo
@ -710,15 +710,15 @@ src/library.cpp and src/library.h.
<P>See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in <A HREF = "Section_howto.html#4_10">this section</A> of the manual.
discussed in <A HREF = "Section_howto.html#howto_10">this section</A> of the manual.
See <A HREF = "Section_python.html">this section</A> of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
</P>
<P>The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See <A HREF = "Section_howto.html#4_19">this section</A> of the manual
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See <A HREF = "Section_howto.html#howto_19">this section</A> of the
manual for a description of the interface and how to extend it for
your needs.
</P>
<HR>
@ -925,13 +925,13 @@ processors.
</P>
<P>Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running <A HREF = "Section_howto.html#4_5">multi-replica
This can be useful for running <A HREF = "Section_howto.html#howto_5">multi-replica
simulations</A>, on one or a few processors.
</P>
<P>The input script specifies what simulation is run on which partition;
see the <A HREF = "variable.html">variable</A> and <A HREF = "next.html">next</A> commands. This
<A HREF = "Section_howto.html#4_4">howto section</A> gives examples of how to use
these commands in this way. Simulations running on different
<A HREF = "Section_howto.html#howto_4">howto section</A> gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
<A HREF = "temper.html">temper</A> command.
</P>
@ -1016,9 +1016,9 @@ value2 ..." at the beginning of the input script. Defining an index
variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the <A HREF = "variable.html">variable</A> command for more info on
defining index and other kinds of variables and <A HREF = "Section_commands.html#3_2">this
section</A> for more info on using variables in
input scripts.
defining index and other kinds of variables and <A HREF = "Section_commands.html#cmd_2">this
section</A> for more info on using variables
in input scripts.
</P>
<HR>

22
doc/Section_start.txt
View File

@ -676,8 +676,8 @@ build will likely fail.
LAMMPS itself can be built as a library, which can then be called from
another application or a scripting language. See "this
section"_Section_howto.html#4_10 for more info on coupling LAMMPS to
other codes. Building LAMMPS as a library is done by typing
section"_Section_howto.html#howto_10 for more info on coupling LAMMPS
to other codes. Building LAMMPS as a library is done by typing
make makelib
make -f Makefile.lib foo :pre
@ -703,15 +703,15 @@ src/library.cpp and src/library.h.
See the sample codes couple/simple/simple.cpp and simple.c as examples
of C++ and C codes that invoke LAMMPS thru its library interface.
There are other examples as well in the couple directory which are
discussed in "this section"_Section_howto.html#4_10 of the manual.
discussed in "this section"_Section_howto.html#howto_10 of the manual.
See "this section"_Section_python.html of the manual for a description
of the Python wrapper provided with LAMMPS that operates through the
LAMMPS library interface.
The files src/library.cpp and library.h contain the C-style interface
to LAMMPS. See "this section"_Section_howto.html#4_19 of the manual
for a description of the interface and how to extend it for your
needs.
to LAMMPS. See "this section"_Section_howto.html#howto_19 of the
manual for a description of the interface and how to extend it for
your needs.
:line
@ -916,12 +916,12 @@ processors.
Note that with MPI installed on a machine (e.g. your desktop), you can
run on more (virtual) processors than you have physical processors.
This can be useful for running "multi-replica
simulations"_Section_howto.html#4_5, on one or a few processors.
simulations"_Section_howto.html#howto_5, on one or a few processors.
The input script specifies what simulation is run on which partition;
see the "variable"_variable.html and "next"_next.html commands. This
"howto section"_Section_howto.html#4_4 gives examples of how to use
these commands in this way. Simulations running on different
"howto section"_Section_howto.html#howto_4 gives examples of how to
use these commands in this way. Simulations running on different
partitions can also communicate with each other; see the
"temper"_temper.html command.
@ -1007,8 +1007,8 @@ variable as a command-line argument overrides any setting for the same
index variable in the input script, since index variables cannot be
re-defined. See the "variable"_variable.html command for more info on
defining index and other kinds of variables and "this
section"_Section_commands.html#3_2 for more info on using variables in
input scripts.
section"_Section_commands.html#cmd_2 for more info on using variables
in input scripts.
:line

2
doc/angle_coeff.html
View File

@ -81,7 +81,7 @@ specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command
</UL>
<P>There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/angle_coeff.txt
View File

@ -79,7 +79,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

8
doc/angle_cosine_periodic.html
View File

@ -23,10 +23,10 @@ angle_coeff * 75.0 1 6
<P><B>Description:</B>
</P>
<P>The <I>cosine/periodic</I> angle style uses the following potential, which
is commonly used in the <A HREF = "Section_howto.html#4_4">DREIDING</A> force field,
particularly for organometallic systems where <I>n</I> = 4 might be used
for an octahedral complex and <I>n</I> = 3 might be used for a trigonal
center:
is commonly used in the <A HREF = "Section_howto.html#howto_4">DREIDING</A> force
field, particularly for organometallic systems where <I>n</I> = 4 might be
used for an octahedral complex and <I>n</I> = 3 might be used for a
trigonal center:
</P>
<CENTER><IMG SRC = "Eqs/angle_cosine_periodic.jpg">
</CENTER>

8
doc/angle_cosine_periodic.txt
View File

@ -20,10 +20,10 @@ angle_coeff * 75.0 1 6 :pre
[Description:]
The {cosine/periodic} angle style uses the following potential, which
is commonly used in the "DREIDING"_Section_howto.html#4_4 force field,
particularly for organometallic systems where {n} = 4 might be used
for an octahedral complex and {n} = 3 might be used for a trigonal
center:
is commonly used in the "DREIDING"_Section_howto.html#howto_4 force
field, particularly for organometallic systems where {n} = 4 might be
used for an octahedral complex and {n} = 3 might be used for a
trigonal center:
:c,image(Eqs/angle_cosine_periodic.jpg)

2
doc/angle_style.html
View File

@ -73,7 +73,7 @@ specified by the associated <A HREF = "angle_coeff.html">angle_coeff</A> command
</UL>
<P>There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the angle section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/angle_style.txt
View File

@ -72,7 +72,7 @@ specified by the associated "angle_coeff"_angle_coeff.html command:
There are also additional angle styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the angle section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

2
doc/bond_coeff.html
View File

@ -77,7 +77,7 @@ specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</UL>
<P>There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/bond_coeff.txt
View File

@ -75,7 +75,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

2
doc/bond_style.html
View File

@ -82,7 +82,7 @@ specified by the associated <A HREF = "bond_coeff.html">bond_coeff</A> command:
</UL>
<P>There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the bond section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<HR>

2
doc/bond_style.txt
View File

@ -80,7 +80,7 @@ specified by the associated "bond_coeff"_bond_coeff.html command:
There are also additional bond styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the bond section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
:line

8
doc/change_box.html
View File

@ -28,7 +28,7 @@ change_box triclinic
<P><B>Description:</B>
</P>
<P>By default LAMMPS runs a simulation in an orthogonal, axis-aligned
simulation box. LAMMPS can also run simulations in <A HREF = "Section_howto.html#4_12">non-orthogonal
simulation box. LAMMPS can also run simulations in <A HREF = "Section_howto.html#howto_12">non-orthogonal
(triclinic) simulation boxes</A>. A box is
defined as either orthogonal or non-orthogonal when it is created via
the <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_data</A>, or
@ -37,9 +37,9 @@ the <A HREF = "create_box.html">create_box</A>, <A HREF = "read_data.html">read_
<P>This command allows you to toggle the existing simulation box from
orthogonal to non-orthogonal and vice versa. For example, an initial
equilibration simulation can be run in an orthogonal box, the box can
be toggled to non-orthogonal, and then a <A HREF = "Section_howto.html#4_13">non-equilibrium MD (NEMD)
simulation</A> can be run with deformation via
the <A HREF = "fix_deform.html">fix deform</A> command.
be toggled to non-orthogonal, and then a <A HREF = "Section_howto.html#howto_13">non-equilibrium MD (NEMD)
simulation</A> can be run with deformation
via the <A HREF = "fix_deform.html">fix deform</A> command.
</P>
<P>Note that if the simulation box is currently non-orthogonal and has
non-zero tilt in xy, yz, or xz, then it cannot be converted to an

6
doc/change_box.txt
View File

@ -25,7 +25,7 @@ change_box triclinic :pre
By default LAMMPS runs a simulation in an orthogonal, axis-aligned
simulation box. LAMMPS can also run simulations in "non-orthogonal
(triclinic) simulation boxes"_Section_howto.html#4_12. A box is
(triclinic) simulation boxes"_Section_howto.html#howto_12. A box is
defined as either orthogonal or non-orthogonal when it is created via
the "create_box"_create_box.html, "read_data"_read_data.html, or
"read_restart"_read_restart.html commands.
@ -34,8 +34,8 @@ This command allows you to toggle the existing simulation box from
orthogonal to non-orthogonal and vice versa. For example, an initial
equilibration simulation can be run in an orthogonal box, the box can
be toggled to non-orthogonal, and then a "non-equilibrium MD (NEMD)
simulation"_Section_howto.html#4_13 can be run with deformation via
the "fix deform"_fix_deform.html command.
simulation"_Section_howto.html#howto_13 can be run with deformation
via the "fix deform"_fix_deform.html command.
Note that if the simulation box is currently non-orthogonal and has
non-zero tilt in xy, yz, or xz, then it cannot be converted to an

6
doc/compute.html
View File

@ -36,7 +36,7 @@ information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
See this <A HREF = "Section_howto.html#4_15">howto section</A> for a summary of
See this <A HREF = "Section_howto.html#howto_15">howto section</A> for a summary of
various LAMMPS output options, many of which involve computes.
</P>
<P>The ID of a compute can only contain alphanumeric characters and
@ -217,13 +217,13 @@ available in LAMMPS:
</UL>
<P>There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the compute section of <A HREF = "Section_commands.html#3_5">this
the individual styles are given in the compute section of <A HREF = "Section_commands.html#cmd_5">this
page</A>.
</P>
<P>There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs and GPUs. The list
of these with links to the individual styles are given in the pair
section of <A HREF = "Section_commands.html#3_5">this page</A>.
section of <A HREF = "Section_commands.html#cmd_5">this page</A>.
</P>
<P><B>Restrictions:</B> none
</P>

6
doc/compute.txt
View File

@ -33,7 +33,7 @@ information about a previous state of the system. Defining a compute
does not perform a computation. Instead computes are invoked by other
LAMMPS commands as needed, e.g. to calculate a temperature needed for
a thermostat fix or to generate thermodynamic or dump file output.
See this "howto section"_Section_howto.html#4_15 for a summary of
See this "howto section"_Section_howto.html#howto_15 for a summary of
various LAMMPS output options, many of which involve computes.
The ID of a compute can only contain alphanumeric characters and
@ -213,12 +213,12 @@ available in LAMMPS:
There are also additional compute styles submitted by users which are
included in the LAMMPS distribution. The list of these with links to
the individual styles are given in the compute section of "this
page"_Section_commands.html#3_5.
page"_Section_commands.html#cmd_5.
There are also additional accelerated compute styles included in the
LAMMPS distribution for faster performance on CPUs and GPUs. The list
of these with links to the individual styles are given in the pair
section of "this page"_Section_commands.html#3_5.
section of "this page"_Section_commands.html#cmd_5.
[Restrictions:] none

4
doc/compute_ackland_atom.html
View File

@ -53,8 +53,8 @@ which computes this quantity.-
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom values from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P><B>Restrictions:</B>
</P>

4
doc/compute_ackland_atom.txt
View File

@ -50,8 +50,8 @@ which computes this quantity.-
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom values from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
[Restrictions:]

2
doc/compute_angle_local.html
View File

@ -67,7 +67,7 @@ array is the number of angles. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_angle_local.txt
View File

@ -60,7 +60,7 @@ local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The output for {theta} will be in degrees. The output for {eng} will

2
doc/compute_atom_molecule.html
View File

@ -97,7 +97,7 @@ rows in the array is the number of molecules. If a single input is
specified, a global vector is produced. If two or more inputs are
specified, a global array is produced where the number of columns =
the number of inputs. The vector or array can be accessed by any
command that uses global values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
command that uses global values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_atom_molecule.txt
View File

@ -90,7 +90,7 @@ specified, a global vector is produced. If two or more inputs are
specified, a global array is produced where the number of columns =
the number of inputs. The vector or array can be accessed by any
command that uses global values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
All the vector or array values calculated by this compute are

2
doc/compute_bond_local.html
View File

@ -66,7 +66,7 @@ array is the number of bonds. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_bond_local.txt
View File

@ -59,7 +59,7 @@ local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The

2
doc/compute_centro_atom.html
View File

@ -79,7 +79,7 @@ too frequently or to have multiple compute/dump commands, each with a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values are unitless values >= 0.0. Their

2
doc/compute_centro_atom.txt
View File

@ -75,7 +75,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values are unitless values >= 0.0. Their

2
doc/compute_cluster_atom.html
View File

@ -46,7 +46,7 @@ too frequently or to have multiple compute/dump commands, each of a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be an ID > 0, as explained above.

2
doc/compute_cluster_atom.txt
View File

@ -43,7 +43,7 @@ too frequently or to have multiple compute/dump commands, each of a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be an ID > 0, as explained above.

2
doc/compute_cna_atom.html
View File

@ -77,7 +77,7 @@ too frequently or to have multiple compute/dump commands, each with a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be a number from 0 to 5, as explained

2
doc/compute_cna_atom.txt
View File

@ -74,7 +74,7 @@ too frequently or to have multiple compute/dump commands, each with a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be a number from 0 to 5, as explained

5
doc/compute_com.html
View File

@ -52,8 +52,9 @@ file</A> containing coordinates of the atoms in the bodies.
</P>
<P>This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values are "intensive". The vector values will be in
distance <A HREF = "units.html">units</A>.

5
doc/compute_com.txt
View File

@ -49,8 +49,9 @@ file"_dump.html containing coordinates of the atoms in the bodies.
This compute calculates a global vector of length 3, which can be
accessed by indices 1-3 by any command that uses global vector values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values are "intensive". The vector values will be in
distance "units"_units.html.

2
doc/compute_com_molecule.html
View File

@ -64,7 +64,7 @@ file</A> containing coordinates of the atoms in the bodies.
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
coordinates of each molecule. These values can be accessed by any
command that uses global array values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The array values are "intensive". The array values will be in

2
doc/compute_com_molecule.txt
View File

@ -61,7 +61,7 @@ This compute calculates a global array where the number of rows =
Nmolecules and the number of columns = 3 for the x,y,z center-of-mass
coordinates of each molecule. These values can be accessed by any
command that uses global array values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The array values are "intensive". The array values will be in

2
doc/compute_coord_atom.html
View File

@ -46,7 +46,7 @@ too frequently or to have multiple compute/dump commands, each of a
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained

2
doc/compute_coord_atom.txt
View File

@ -43,7 +43,7 @@ too frequently or to have multiple compute/dump commands, each of a
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be a number >= 0.0, as explained

2
doc/compute_damage_atom.html
View File

@ -37,7 +37,7 @@ compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be a number >= 0.0, as explained

2
doc/compute_damage_atom.txt
View File

@ -34,7 +34,7 @@ compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be a number >= 0.0, as explained

2
doc/compute_dihedral_local.html
View File

@ -60,7 +60,7 @@ array is the number of dihedrals. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_dihedral_local.txt
View File

@ -53,7 +53,7 @@ local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The output for {phi} will be in degrees.

4
doc/compute_displace_atom.html
View File

@ -76,8 +76,8 @@ file.
</P>
<P>This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
</P>
<P>The per-atom array values will be in distance <A HREF = "units.html">units</A>.
</P>

4
doc/compute_displace_atom.txt
View File

@ -73,8 +73,8 @@ file.
This compute calculates a per-atom array with 4 columns, which can be
accessed by indices 1-4 by any command that uses per-atom values from
a compute as input. See "this section"_Section_howto.html#4_15 for an
overview of LAMMPS output options.
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The per-atom array values will be in distance "units"_units.html.

4
doc/compute_erotate_asphere.html
View File

@ -39,8 +39,8 @@ the same as in 3d.
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_erotate_asphere.txt
View File

@ -36,8 +36,8 @@ the same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_erotate_sphere.html
View File

@ -38,8 +38,8 @@ same as in 3d.
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_erotate_sphere.txt
View File

@ -35,8 +35,8 @@ same as in 3d.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

4
doc/compute_event_displace.html
View File

@ -46,8 +46,8 @@ local atom displacements and may generate "false postives."
</P>
<P>This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.

4
doc/compute_event_displace.txt
View File

@ -43,8 +43,8 @@ local atom displacements and may generate "false postives."
This compute calculates a global scalar (the flag). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
scalar value will be a 0 or 1 as explained above.

2
doc/compute_group_group.html
View File

@ -44,7 +44,7 @@ quantity too frequently.
<P>This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_group_group.txt
View File

@ -42,7 +42,7 @@ This compute calculates a global scalar (the energy) and a global
vector of length 3 (force), which can be accessed by indices 1-3.
These values can be used by any command that uses global scalar or
vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
Both the scalar and vector values calculated by this compute are

4
doc/compute_gyration.html
View File

@ -49,8 +49,8 @@ image</A> command.
</P>
<P>This compute calculates a global scalar (Rg). This value can be used
by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "intensive". The
scalar value will be in distance <A HREF = "units.html">units</A>.

4
doc/compute_gyration.txt
View File

@ -46,8 +46,8 @@ image"_set.html command.
This compute calculates a global scalar (Rg). This value can be used
by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "intensive". The
scalar value will be in distance "units"_units.html.

2
doc/compute_gyration_molecule.html
View File

@ -62,7 +62,7 @@ image</A> command.
</P>
<P>This compute calculates a global vector of Rg values where the length
of the vector = Nmolecules. These values can be used by any command
that uses global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
that uses global vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_gyration_molecule.txt
View File

@ -60,7 +60,7 @@ image"_set.html command.
This compute calculates a global vector of Rg values where the length
of the vector = Nmolecules. These values can be used by any command
that uses global vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values calculated by this compute are "intensive". The

2
doc/compute_heat_flux.html
View File

@ -99,7 +99,7 @@ result should be: average conductivity ~0.29 in W/mK.
<P>This compute calculates a global vector of length 6 (total heat flux
vector, followed by conductive heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
uses global vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses global vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_heat_flux.txt
View File

@ -97,7 +97,7 @@ This compute calculates a global vector of length 6 (total heat flux
vector, followed by conductive heat flux vector), which can be
accessed by indices 1-6. These values can be used by any command that
uses global vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values calculated by this compute are "extensive", meaning

2
doc/compute_improper_local.html
View File

@ -60,7 +60,7 @@ array is the number of impropers. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_improper_local.txt
View File

@ -53,7 +53,7 @@ local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The output for {chi} will be in degrees.

4
doc/compute_ke.html
View File

@ -47,8 +47,8 @@ include different degrees of freedom (translational, rotational, etc).
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_ke.txt
View File

@ -44,8 +44,8 @@ include different degrees of freedom (translational, rotational, etc).
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

2
doc/compute_ke_atom.html
View File

@ -37,7 +37,7 @@ specified compute group.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.

2
doc/compute_ke_atom.txt
View File

@ -34,7 +34,7 @@ specified compute group.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/compute_ke_atom_eff.html
View File

@ -62,7 +62,7 @@ electrons) not in the specified compute group.
</P>
<P>This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.

2
doc/compute_ke_atom_eff.txt
View File

@ -59,7 +59,7 @@ electrons) not in the specified compute group.
This compute calculates a scalar quantity for each atom, which can be
accessed by any command that uses per-atom computes as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be in energy "units"_units.html.

4
doc/compute_ke_eff.html
View File

@ -64,8 +64,8 @@ thermo_modify temp effTemp
</P>
<P>This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of
LAMMPS output options.
input. See <A HREF = "Section_howto.html#howto_15">this section</A> for an overview
of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_ke_eff.txt
View File

@ -61,8 +61,8 @@ See "compute temp/eff"_compute_temp_eff.html.
This compute calculates a global scalar (the KE). This value can be
used by any command that uses a global scalar value from a compute as
input. See "this section"_Section_howto.html#4_15 for an overview of
LAMMPS output options.
input. See "this section"_Section_howto.html#howto_15 for an overview
of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

5
doc/compute_msd.html
View File

@ -92,8 +92,9 @@ file.
</P>
<P>This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The vector values are "intensive". The vector values will be in
distance^2 <A HREF = "units.html">units</A>.

5
doc/compute_msd.txt
View File

@ -84,8 +84,9 @@ file.
This compute calculates a global vector of length 4, which can be
accessed by indices 1-4 by any command that uses global vector values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector values are "intensive". The vector values will be in
distance^2 "units"_units.html.

2
doc/compute_msd_molecule.html
View File

@ -81,7 +81,7 @@ file</A>.
<P>This compute calculates a global array where the number of rows =
Nmolecules and the number of columns = 4 for dx,dy,dz and the total
displacement. These values can be accessed by any command that uses
global array values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
global array values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_msd_molecule.txt
View File

@ -79,7 +79,7 @@ This compute calculates a global array where the number of rows =
Nmolecules and the number of columns = 4 for dx,dy,dz and the total
displacement. These values can be accessed by any command that uses
global array values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The array values are "intensive". The array values will be in

5
doc/compute_pair.html
View File

@ -62,8 +62,9 @@ are stored as a global vector by this compute. See the doc page for
<I>ecoul</I>. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. These values
can be used by any command that uses global scalar or vector values
from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A>
for an overview of LAMMPS output options.
from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>
<P>The scalar and vector values calculated by this compute are
"extensive".

5
doc/compute_pair.txt
View File

@ -59,8 +59,9 @@ This compute calculates a global scalar which is {epair} or {evdwl} or
{ecoul}. If the pair style supports it, it also calculates a global
vector of length >= 1, as determined by the pair style. These values
can be used by any command that uses global scalar or vector values
from a compute as input. See "this section"_Section_howto.html#4_15
for an overview of LAMMPS output options.
from a compute as input. See "this
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are
"extensive".

2
doc/compute_pair_local.html
View File

@ -80,7 +80,7 @@ array is the number of pairs. If a single keyword is specified, a
local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
uses local values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_pair_local.txt
View File

@ -73,7 +73,7 @@ local vector is produced. If two or more keywords are specified, a
local array is produced where the number of columns = the number of
keywords. The vector or array can be accessed by any command that
uses local values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The output for {dist} will be in distance "units"_units.html. The

4
doc/compute_pe.html
View File

@ -83,8 +83,8 @@ instructions on how to use the accelerated styles effectively.
</P>
<P>This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an
overview of LAMMPS output options.
a compute as input. See <A HREF = "Section_howto.html#howto_15">this section</A>
for an overview of LAMMPS output options.
</P>
<P>The scalar value calculated by this compute is "extensive". The
scalar value will be in energy <A HREF = "units.html">units</A>.

4
doc/compute_pe.txt
View File

@ -79,8 +79,8 @@ instructions on how to use the accelerated styles effectively.
This compute calculates a global scalar (the potential energy). This
value can be used by any command that uses a global scalar value from
a compute as input. See "this section"_Section_howto.html#4_15 for an
overview of LAMMPS output options.
a compute as input. See "this section"_Section_howto.html#howto_15
for an overview of LAMMPS output options.
The scalar value calculated by this compute is "extensive". The
scalar value will be in energy "units"_units.html.

2
doc/compute_pe_atom.html
View File

@ -70,7 +70,7 @@ the system energy.
</P>
<P>This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
<A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS
<A HREF = "Section_howto.html#howto_15">this section</A> for an overview of LAMMPS
output options.
</P>
<P>The per-atom vector values will be in energy <A HREF = "units.html">units</A>.

2
doc/compute_pe_atom.txt
View File

@ -67,7 +67,7 @@ the system energy.
This compute calculates a per-atom vector, which can be accessed by
any command that uses per-atom values from a compute as input. See
"this section"_Section_howto.html#4_15 for an overview of LAMMPS
"this section"_Section_howto.html#howto_15 for an overview of LAMMPS
output options.
The per-atom vector values will be in energy "units"_units.html.

2
doc/compute_pressure.html
View File

@ -114,7 +114,7 @@ instructions on how to use the accelerated styles effectively.
<P>This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
or vector values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

2
doc/compute_pressure.txt
View File

@ -111,7 +111,7 @@ This compute calculates a global scalar (the pressure) and a global
vector of length 6 (pressure tensor), which can be accessed by indices
1-6. These values can be used by any command that uses global scalar
or vector values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The scalar and vector values calculated by this compute are

4
doc/compute_property_atom.html
View File

@ -67,7 +67,7 @@ compute 1 all property/atom ix iy iz
</P>
<P>Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
<A HREF = "Section_howto.html#4_15">output commands</A> that take computes as
<A HREF = "Section_howto.html#howto_15">output commands</A> that take computes as
inputs. See for example, the <A HREF = "compute_reduce.html">compute reduce</A>,
<A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix ave/histo</A>,
<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>, and <A HREF = "variable.html">atom-style
@ -100,7 +100,7 @@ on the number of input values. If a single input is specified, a
per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
per-atom values from a compute as input. See <A HREF = "Section_howto.html#4_15">this
per-atom values from a compute as input. See <A HREF = "Section_howto.html#howto_15">this
section</A> for an overview of LAMMPS output
options.
</P>

4
doc/compute_property_atom.txt
View File

@ -60,7 +60,7 @@ compute 1 all property/atom ix iy iz :pre
Define a computation that simply stores atom attributes for each atom
in the group. This is useful so that the values can be used by other
"output commands"_Section_howto.html#4_15 that take computes as
"output commands"_Section_howto.html#howto_15 that take computes as
inputs. See for example, the "compute reduce"_compute_reduce.html,
"fix ave/atom"_fix_ave_atom.html, "fix ave/histo"_fix_ave_histo.html,
"fix ave/spatial"_fix_ave_spatial.html, and "atom-style
@ -94,7 +94,7 @@ per-atom vector is produced. If two or more inputs are specified, a
per-atom array is produced where the number of columns = the number of
inputs. The vector or array can be accessed by any command that uses
per-atom values from a compute as input. See "this
section"_Section_howto.html#4_15 for an overview of LAMMPS output
section"_Section_howto.html#howto_15 for an overview of LAMMPS output
options.
The vector or array values will be in whatever "units"_units.html the

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